A method for estimating cathode inlet and cathode outlet relative humidity (RH) of a fuel cell stack. The method uses a model to estimate the high frequency resistance (HFR) of the fuel cell stack based on water specie balance, and also measures stack HFR. The HFR values from the estimated HFR and the measured HFR are compared, and an error between the HFR values is determined. An online regression algorithm is then utilized to minimize the error and the solution of the regression is the RH profile in the stack including the cathode inlet and outlet relative humidities.